RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11794
(325 letters)
>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug
design, transferase; 2.35A {Human immunodeficiency virus
2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B
Length = 555
Score = 47.0 bits (112), Expect = 4e-06
Identities = 27/88 (30%), Positives = 41/88 (46%), Gaps = 13/88 (14%)
Query: 107 TTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLI 166
TT AEL A + L + S ++ II DS V+ I S P S ++ I
Sbjct: 471 TTNQQAELEAFAMALTD-----SGPKVNIIVDSQYVM----GIVASQPTES-ESKIVNQI 520
Query: 167 V--TRGTDVVFL-WCPSHCGIDGNEAVD 191
+ + +++ W P+H GI GN+ VD
Sbjct: 521 IEEMIKKEAIYVAWVPAHKGIGGNQEVD 548
>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI,
nonnucleoside inhibitor, AIDS, HIV, rilpivirine,
diarylpyrimidine, DAPY, DNA recombination; HET: T27;
1.80A {Human immunodeficiency virus 1} PDB: 3is9_A*
3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A
1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A*
2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...
Length = 557
Score = 45.5 bits (108), Expect = 1e-05
Identities = 29/89 (32%), Positives = 46/89 (51%), Gaps = 15/89 (16%)
Query: 107 TTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISK---IYQLW 163
TT EL A+YL L++ S + I++DS L I + P S+ + Q+
Sbjct: 474 TTNQKTELQAIYLALQD-----SGLEVNIVTDSQYAL----GIIQAQPDKSESELVNQII 524
Query: 164 KLIVTRGTDVVFL-WCPSHCGIDGNEAVD 191
+ ++ + + V+L W P+H GI GNE VD
Sbjct: 525 EQLIKK--EKVYLAWVPAHKGIGGNEQVD 551
>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV,
RNAse H, reverse transcriptase, transcription; 1.50A
{Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A
3v1r_A* 2hb5_A
Length = 165
Score = 42.1 bits (99), Expect = 5e-05
Identities = 18/92 (19%), Positives = 29/92 (31%), Gaps = 14/92 (15%)
Query: 112 AELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLI---VT 168
AEL+AL LK ++ + +DS + K + +
Sbjct: 66 AELIALTQALKMAEG----KKLNVYTDSRYAFATAHVHSEGRE--IKNKNEILALLKALF 119
Query: 169 RGTDVVFLWCPSHCGID-----GNEAVDSAAN 195
+ + CP H + GN D AA
Sbjct: 120 LPKRLSIIHCPGHQKGNSAEARGNRMADQAAR 151
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 42.5 bits (99), Expect = 2e-04
Identities = 32/168 (19%), Positives = 59/168 (35%), Gaps = 43/168 (25%)
Query: 32 CWWSNKTY-LHHENFSVMLLLGTLRKLIN-YTLHLQSVMQLFIFH--IDTDTAYRLQENR 87
T + + L KL N Y LH +S++ + D+D ++
Sbjct: 419 KQPKESTISIPS------IYLELKVKLENEYALH-RSIVDHYNIPKTFDSDDLIPPYLDQ 471
Query: 88 YSCCYLGTLVGPGPRYFNLTTIYLAELLA----LYLCLKEISE--FHSSSRIAIISDSLS 141
Y ++G +L I E + ++L + + + H S+ L+
Sbjct: 472 YFYSHIG---------HHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILN 522
Query: 142 VLSALGN----ICFSHP-----------FISKIYQLWKLIVTRGTDVV 174
L L IC + P F+ KI + LI ++ TD++
Sbjct: 523 TLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEE--NLICSKYTDLL 568
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 38.9 bits (90), Expect = 0.002
Identities = 46/274 (16%), Positives = 87/274 (31%), Gaps = 99/274 (36%)
Query: 110 YLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIVTR 169
Y EL LY + I +++LS L + K++ T+
Sbjct: 169 YFEELRDLY----QTYHVLVGDLIKFSAETLSELIR------TTLDAEKVF-------TQ 211
Query: 170 GTDVVFLW------CPSHCGIDGNEAVDSAA-----------NHHTHPRHVNLCSTDDLK 212
G +++ W P + + S H+ + + +L+
Sbjct: 212 GLNIL-EWLENPSNTPD------KDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELR 264
Query: 213 PWIKAI--VKKDIVDMWNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRL-RIGHTR 269
++K + +V ++ + DSW SF + + +T L IG R
Sbjct: 265 SYLKGATGHSQGLV---TAVAIA--------ETDSW-ESFFVSVRK--AITVLFFIG-VR 309
Query: 270 VTHNHLFKKLPPPICQCGSV----------LTVV---------HILECPTLTPAR----I 306
+ LPP I + S+ L++ ++ + + PA I
Sbjct: 310 CYEAYPNTSLPPSILE-DSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEI 368
Query: 307 SL--SPQPNL---G----------ALHETKSTTG 325
SL + NL G L + K+ +G
Sbjct: 369 SLVNGAK-NLVVSGPPQSLYGLNLTLRKAKAPSG 401
Score = 28.9 bits (64), Expect = 3.2
Identities = 33/176 (18%), Positives = 57/176 (32%), Gaps = 64/176 (36%)
Query: 105 NLT--T---IYLAELLALYLCLKE------ISEF--HSSSRIAIISDSL---SVLSALGN 148
+ T T + L E A + LK + F HS L + L++L +
Sbjct: 1727 SATQFTQPALTLMEK-AAFEDLKSKGLIPADATFAGHS----------LGEYAALASLAD 1775
Query: 149 ICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVNL-CS 207
+ S I L +++ RG + P N + A N P V S
Sbjct: 1776 V-MS------IESLVEVVFYRGMTMQVA-VPRDELGRSNYGM-IAIN----PGRVAASFS 1822
Query: 208 TDDLKPWIKAIVKKD-----IV------------------DMWNSIPPSNKLKRIK 240
+ L+ ++ + K+ IV D ++ KL++I
Sbjct: 1823 QEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKID 1878
Score = 27.3 bits (60), Expect = 8.0
Identities = 24/134 (17%), Positives = 46/134 (34%), Gaps = 27/134 (20%)
Query: 53 TLRKLINYTLHLQSVMQLFIFHIDTDT---AYRLQENRYSCCYLGTLVGPGPRY-FNLTT 108
+ R L TL S+ + + T + A +LQE + L P + +
Sbjct: 5 STRPL---TLSHGSLE--HVLLVPTASFFIASQLQE-----QFNKILPEPTEGFAADDEP 54
Query: 109 IYLAELLALYL--CLKEISEFHSSSRIAIISDSL-----SVLSALGN-ICFSHPFISKIY 160
AEL+ +L + +++ L L GN I H +K+
Sbjct: 55 TTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLE--GNDI---HALAAKLL 109
Query: 161 QLWKLIVTRGTDVV 174
Q + + +++
Sbjct: 110 QENDTTLVKTKELI 123
>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO
enzyme, structural genomics, protein structure
initiative; NMR {Desulfitobacterium hafniense dcb-2}
PDB: 2kw4_A
Length = 147
Score = 36.6 bits (85), Expect = 0.003
Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 6/85 (7%)
Query: 112 AELLALYLCLKEISEFHSSSRIAIISDSLSVLS-ALGNICFSHPFISKIYQLWKLIVTRG 170
E+ A +K+ S+ +I I+ D + A G + F +L
Sbjct: 53 GEIAAALYAVKKASQ--LGVKIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQY---R 107
Query: 171 TDVVFLWCPSHCGIDGNEAVDSAAN 195
F +H G + N+ VD A
Sbjct: 108 GIYSFEKVKAHSGNEFNDYVDMKAK 132
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 32.2 bits (74), Expect = 0.095
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 162 LWKLI--VTRGTDVVFLWCPSHCGIDGNEAVDSAAN 195
+ + +T+G D+ ++ P H G GNE D A
Sbjct: 111 DFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAR 146
>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase,
hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} PDB:
3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A
Length = 150
Score = 31.4 bits (72), Expect = 0.20
Identities = 26/100 (26%), Positives = 36/100 (36%), Gaps = 25/100 (25%)
Query: 112 AELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKI------------ 159
EL A+YL L++ S + I++DS L I K
Sbjct: 52 TELQAIYLALQD-----SGLEVNIVTDSQYAL----GIITQWIHNWKKRGWKTADKKPVK 102
Query: 160 -YQLWKLI---VTRGTDVVFLWCPSHCGIDGNEAVDSAAN 195
L I + + V W P+H GI GNE VD +
Sbjct: 103 NVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVS 142
>3oqu_A Abscisic acid receptor PYL9; RCAR1, hormone receptor; HET: A8S;
2.68A {Arabidopsis thaliana}
Length = 205
Score = 28.2 bits (62), Expect = 2.7
Identities = 13/64 (20%), Positives = 25/64 (39%), Gaps = 5/64 (7%)
Query: 182 CGIDGNEAVDSAANHHTHPRHVNLCSTDDLKPWIKAIVKKDIVDMWNSIPPSNKLKRIKP 241
G E V HH H N C++ + +K + +W+ + ++ ++ KP
Sbjct: 28 AMYGGLETVQYVRTHHQHLCRENQCTSA-----LVKHIKAPLHLVWSLVRRFDQPQKYKP 82
Query: 242 TVDS 245
V
Sbjct: 83 FVSR 86
>3rt2_A Abscisic acid receptor PYL10; ABA-independent PP2C inhibitor,
PP2CS, hydrolase inhibitor; 1.50A {Arabidopsis thaliana}
PDB: 3r6p_A* 3qtj_A* 3uqh_A 3rt0_C
Length = 183
Score = 28.1 bits (62), Expect = 3.2
Identities = 10/66 (15%), Positives = 25/66 (37%), Gaps = 6/66 (9%)
Query: 180 SHCGIDGNEAVDSAANHHTHPRHVNLCSTDDLKPWIKAIVKKDIVDMWNSIPPSNKLKRI 239
+ E+ + HH H + CS + +K + +W+ + ++ ++
Sbjct: 2 NGDETKKVES-EYIKKHHRHELVESQCS-----STLVKHIKAPLHLVWSIVRRFDEPQKY 55
Query: 240 KPTVDS 245
KP +
Sbjct: 56 KPFISR 61
>2x7j_A 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene -1-carboxylate
synthase; transferase, metal-binding; HET: TPP; 2.35A
{Bacillus subtilis}
Length = 604
Score = 28.3 bits (63), Expect = 4.1
Identities = 18/133 (13%), Positives = 33/133 (24%), Gaps = 1/133 (0%)
Query: 187 NEAVDSAANHHTHPRHVNLCSTDDLKPWIKAIVKKDIVDMWNSIPPSNKLKRIKPTVDSW 246
+ A A P HVN+ + L P + + + + + ++
Sbjct: 177 SRAAGEAQKRPMGPVHVNVPLREPLMPDLSDEPFGRMRTGRHVSVKTGTQSVDRESLSDV 236
Query: 247 TSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLP-PPICQCGSVLTVVHILECPTLTPAR 305
+V L + L K L P + S L + +
Sbjct: 237 AEMLAEAEKGMIVCGELHSDADKENIIALSKALQYPILADPLSNLRNGVHDKSTVIDAYD 296
Query: 306 ISLSPQPNLGALH 318
L L
Sbjct: 297 SFLKDDELKRKLR 309
>3k3k_A Abscisic acid receptor PYR1; ABA receptor, plant hormone receptor,
A sensor, drought tolerance, plant development; HET:
A8S; 1.70A {Arabidopsis thaliana} PDB: 3njo_A* 3qn1_A*
3k90_A* 3jrq_B* 3kdj_A* 3nef_A* 3neg_A* 3nmn_A* 3kay_A*
Length = 211
Score = 27.4 bits (60), Expect = 4.8
Identities = 13/60 (21%), Positives = 25/60 (41%), Gaps = 5/60 (8%)
Query: 186 GNEAVDSAANHHTHPRHVNLCSTDDLKPWIKAIVKKDIVDMWNSIPPSNKLKRIKPTVDS 245
+E +S A HT+ CS+ + I A + +W+ + +K + K + S
Sbjct: 30 RSELKNSIAEFHTYQLDPGSCSSLHAQ-RIHAPPEL----VWSIVRRFDKPQTYKHFIKS 84
>1psw_A ADP-heptose LPS heptosyltransferase II; structural genomics,
NYSGXRC, LPS biosynthetic pathway, PSI, protein
structure initiative; 2.00A {Escherichia coli} SCOP:
c.87.1.7
Length = 348
Score = 27.3 bits (61), Expect = 6.7
Identities = 6/53 (11%), Positives = 16/53 (30%), Gaps = 10/53 (18%)
Query: 132 RIAIISDSLSVLSALGNICFSHPFISKIYQLWK-----LIVTRGTDVVFLWCP 179
+I +I S +G++ S + + ++ + P
Sbjct: 2 KILVIG-----PSWVGDMMMSQSLYRTLQARYPQAIIDVMAPAWCRPLLSRMP 49
>3lq1_A 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene- 1-carboxylate
synthase; menaquinone biosynthesis, sephchc synthase,
structural genomics; 2.60A {Listeria monocytogenes}
Length = 578
Score = 27.5 bits (61), Expect = 7.5
Identities = 9/47 (19%), Positives = 16/47 (34%)
Query: 187 NEAVDSAANHHTHPRHVNLCSTDDLKPWIKAIVKKDIVDMWNSIPPS 233
+ AVD A P H+N + L P ++ + +
Sbjct: 157 SRAVDIAMKTPRGPVHLNFPLREPLVPILEPSPFTATGKKHHHVHIY 203
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.324 0.138 0.443
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,116,186
Number of extensions: 299957
Number of successful extensions: 629
Number of sequences better than 10.0: 1
Number of HSP's gapped: 627
Number of HSP's successfully gapped: 22
Length of query: 325
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 231
Effective length of database: 4,077,219
Effective search space: 941837589
Effective search space used: 941837589
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 57 (25.8 bits)